Instruction for installing and using the scripts of SeqTU Installation 1. Download and install libSVM: The current release (Version 3.17, April 2013) of LIBSVM can be obtained by downloading the zip file or tar.gz file from http://www.csie.ntu.edu.tw/~cjlin/libsvm/ 2. Copy "grid_WCC081812.py" into libsvm-3.17/tools directory. 3. You also need to have R installed and four R packages installed. The four R packages are a. library(grid) b. library(gridBase) c. library(ggplot2) d. library(seqinr) Usage 1. Your strand-specific RNA-seq data need to be mapped to the corresponding genome. In our study, we use Clostridium Thermocellum genome as a reference genome for mapping. 2. The mapped results need to be re-formatted to two-column single-base signals. Please see a sample file named "ssRNAseq.forward.reversed.signals". The first line of the file presents the first position of the genome, and the two numbers separated by TAB are RNA-seq signals of forward strand and reversed strand, respectively. 3. With the "ssRNAseq.forward.reversed.signals" ready, you also need prepare a GFF file and a FASTA file of the corresponding genome for running an R script named "seqTU_101413.r". In our study, we used NC_009012.gff and NC_009012.fna as the GFF file and the FASTA file. 4. The TU identification will be performed by running "seqTU_101413.r". The results then can be post-processed by another R script named "print.final.table_101413.r". Contact If you have any questions, please contact us 1. Wen-Chi Chou wcc957@gmail.com 2. Qin Ma maqin2001@gmail.com